SMTL ID : 9m6p.1

Discovery of a bifunctional PKMYT1-targeting PROTAC empowered by AI-generation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

homo-hexamer

Ligands

6 x 01: 2,4-dimethyl-3-[2-(2-methylpyrimidin-5-yl)-1~{H}-pyrrolo[2,3-b]pyridin-5-yl]phenol

01.1: 15 residues within 4Å: Chain A: L.65, V.73, A.86, K.88, H.110, V.120, T.136, E.137, C.139, G.140, P.141, Q.145, F.189, G.199, D.200 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.65, A:A.86, A:K.88, A:V.120, A:T.136, A:F.189, A:F.189 Hydrogen bonds: A:C.139, A:Q.145, A:D.200 01.3: 16 residues within 4Å: Chain B: L.65, V.73, A.86, K.88, E.106, H.110, V.120, L.134, T.136, E.137, C.139, G.140, P.141, Q.145, F.189, D.200 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.65, B:V.120, B:L.134, B:T.136, B:P.141, B:F.189, B:F.189 Hydrogen bonds: B:E.106, B:E.106, B:T.136, B:C.139, B:Q.145, B:D.200 01.6: 15 residues within 4Å: Chain C: L.65, V.73, A.86, K.88, H.110, V.120, T.136, E.137, C.139, G.140, P.141, Q.145, F.189, G.199, D.200 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:L.65, C:A.86, C:K.88, C:V.120, C:T.136, C:F.189, C:F.189 Hydrogen bonds: C:C.139, C:Q.145, C:D.200 01.8: 16 residues within 4Å: Chain D: L.65, V.73, A.86, K.88, E.106, H.110, V.120, L.134, T.136, E.137, C.139, G.140, P.141, Q.145, F.189, D.200 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:L.65, D:V.120, D:L.134, D:T.136, D:P.141, D:F.189, D:F.189 Hydrogen bonds: D:E.106, D:E.106, D:T.136, D:C.139, D:Q.145, D:D.200 01.11: 15 residues within 4Å: Chain E: L.65, V.73, A.86, K.88, H.110, V.120, T.136, E.137, C.139, G.140, P.141, Q.145, F.189, G.199, D.200 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:L.65, E:A.86, E:K.88, E:V.120, E:T.136, E:F.189, E:F.189 Hydrogen bonds: E:C.139, E:Q.145, E:D.200 01.13: 16 residues within 4Å: Chain F: L.65, V.73, A.86, K.88, E.106, H.110, V.120, L.134, T.136, E.137, C.139, G.140, P.141, Q.145, F.189, D.200 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:L.65, F:V.120, F:L.134, F:T.136, F:P.141, F:F.189, F:F.189 Hydrogen bonds: F:E.106, F:E.106, F:T.136, F:C.139, F:Q.145, F:D.200

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 6 residues within 4Å: Chain A: Q.56, R.61, R.89 Chain B: G.258, E.259, G.260 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.56, B:E.259, B:G.260 Salt bridges: A:R.61, A:R.89 PO4.4: 5 residues within 4Å: Chain A: G.258, E.259 Chain B: Q.56, R.61, R.89 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.61, B:R.89 Hydrogen bonds: A:E.259 PO4.7: 6 residues within 4Å: Chain C: Q.56, R.61, R.89 Chain D: G.258, E.259, G.260 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.56, D:E.259, D:G.260 Salt bridges: C:R.61, C:R.89 PO4.9: 5 residues within 4Å: Chain C: G.258, E.259 Chain D: Q.56, R.61, R.89 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Salt bridges: D:R.61, D:R.89 Hydrogen bonds: C:E.259 PO4.12: 6 residues within 4Å: Chain E: Q.56, R.61, R.89 Chain F: G.258, E.259, G.260 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:Q.56, F:E.259, F:G.260 Salt bridges: E:R.61, E:R.89 PO4.14: 5 residues within 4Å: Chain E: G.258, E.259 Chain F: Q.56, R.61, R.89 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:E.259 Salt bridges: F:R.61, F:R.89

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 2 residues within 4Å: Chain B: N.187, D.200 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain D: N.187, D.200 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain F: N.187, D.200 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y. et al., Discovery of a bifunctional PKMYT1-targeting PROTAC empowered by AI-generation. Nat Commun (2025)

Release Date

2025-11-05

Peptides

Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

C
AAA

D
BBB

E
AAA

F
BBB

Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase

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